Using computer algebra and SMT solvers in algebraic biology

Mateo Pineda Osorio

doi:10.1117/12.2049261

22 May 2014 Using computer algebra and SMT solvers in algebraic biology

Mateo Pineda Osorio

Proceedings Volume 9118, Independent Component Analyses, Compressive Sampling, Wavelets, Neural Net, Biosystems, and Nanoengineering XII; 911810 (2014) https://doi.org/10.1117/12.2049261
Event: SPIE Sensing Technology + Applications, 2014, Baltimore, MD, United States

Abstract

Biologic processes are represented as Boolean networks, in a discrete time. The dynamics within these networks are approached with the help of SMT Solvers and the use of computer algebra. Software such as Maple and Z3 was used in this case. The number of stationary states for each network was calculated. The network studied here corresponds to the immune system under the effects of drastic mood changes. Mood is considered as a Boolean variable that affects the entire dynamics of the immune system, changing the Boolean satisfiability and the number of stationary states of the immune network. Results obtained show Z3’s great potential as a SMT Solver. Some of these results were verified in Maple, even though it showed not to be as suitable for the problem approach. The solving code was constructed using Z3-Python and Z3-SMT-LiB. Results obtained are important in biology systems and are expected to help in the design of immune therapies. As a future line of research, more complex Boolean network representations of the immune system as well as the whole psychological apparatus are suggested.

Citation Download Citation

Mateo Pineda Osorio "Using computer algebra and SMT solvers in algebraic biology", Proc. SPIE 9118, Independent Component Analyses, Compressive Sampling, Wavelets, Neural Net, Biosystems, and Nanoengineering XII, 911810 (22 May 2014); https://doi.org/10.1117/12.2049261

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